Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein

In the present study we examine the thermodynamics of binding of two related pyrazine-derived ligands to the major urinary protein, MUP-I, using a combination of isothermal titration calorimetry (ITC), X-ray crystallography, and NMR backbone (15)N and methyl side-chain (2)H relaxation measurements. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than the classical entropy-driven hydrophobic effect. Unfavorable entropic contributions from the protein backbone and side-chain residues in the vicinity of the binding pocket are partially offset by favorable entropic contributions at adjacent positions, suggesting a "conformational relay" mechanism whereby increased rigidity of residues on ligand binding are accompanied by increased conformational freedom of side chains in adjacent positions. The principal driving force governing ligand affinity and specificity can be attributed to solvent-driven enthalpic effects from desolvation of the protein binding pocket.     

Diboron Bonds Between BX3 (X=H,F, CH3) and BYZ2 (Y=H,F; Z=CO,N2, CNH)

The ability of B atoms on two different molecules to engage with one another in a noncovalent diboron bond is studied by ab initio calculations. Due to electron donation from its substituents, the trivalent B atom of BYZ₂ (Z=CO, N₂, and CNH; Y=H and F) has the ability to in turn donate charge to the B of a BX₃ molecule (X=H, F, and CH₃), thus forming a B⋅⋅⋅B diboron bond. These bonds are of two different strengths and character. BH(CO)₂ and BH(CNH)₂, and their fluorosubstituted analogues BF(CO)₂ and BF(CNH)₂, engage in a typical noncovalent bond with B(CH₃)₃ and BF₃, with interaction energies in the 3–8 kcal/mol range. Certain other combinations result in a much stronger diboron bond, in the 26–44 kcal/mol range, and with a high degree of covalent character. Bonds of this type occur when BH₃ is added to BH(CO)₂, BH(CNH)₂, BH(N₂)₂, and BF(CO)₂, or in the complexes of BH(N₂)₂ with B(CH₃)₃ and BF₃. The weaker noncovalent bonds are held together by roughly equal electrostatic and dispersion components, complemented by smaller polarization energy, while polarization is primarily responsible for the stronger ones.     

Synthesis of Organic-Inorganic Hybrid Particles by Sol-Gel Chemistry

The synthesis of ORganically MOdified SILica (ORMOSIL) particles has been carried out using both the hydrolytic and non-hydrolytic sol-gel routes. The hybrid (nano)composites are organically modified with an alkyl or aryl group covalently bonded to silicon. Hybrids have been synthesised in an aqueous sol-gel process by a modified Stöber route, producing spherical nanoparticles with diameters in the range 50–300 nm. The size of the particles can be controlled by control of certain reaction parameters. Smaller ormosil nanoparticles can be synthesised by a base-catalysed emulsion polymerisation route, by varying the type and concentration of surfactant and precursor feed rate. In this case, particles in the size range 3.5–10 nm can be obtained. Hybrids have been synthesised from hyperbranched polyesters by encapsulation in a silica matrix using the hydrolytic sol-gel route. Optimisation of the reaction conditions allows the hybrids to be produced as isolated sub-micron spherical particles. Ormosil particles have also been synthesised using the non-hydrolytic sol-gel route, which may lead to products of different morphologies because of the different polarity of the reaction medium. Different reaction conditions were studied in order to optimise the size and shape of the particles, including choice of solvent, use of surfactants and addition of polystyrene. Dimethylsulfoxide acts as a novel oxygen donor for the catalyst-free formation of colourless silsesquioxanes.     

Overview of software options for processing,analysis and interpretation of mass spectrometric proteomic data

Recently, the interests in proteomics have been intensively increased, and the proteomic methods have been widely applied to many problems in cell biology. If the age of 1990s is considered to be a decade of genomics, we can claim that the following years of the new century is a decade of proteomics. The rapid evolution of proteomics has continued through these years, with a series of innovations in separation techniques and the core technologies of two‐dimensional gel electrophoresis and MS. Both technologies are fueled by automation and high throughput computation for profiling of proteins from biological systems. As Patterson ever mentioned, ‘data analysis is the Achilles heel of proteomics and our ability to generate data now outstrips our ability to analyze it’. The development of automatic and high throughput technologies for rapid identification of proteins is essential for large‐scale proteome projects and automatic protein identification and characterization is essential for high throughput proteomics. This review provides a snap shot of the tools and applications that are available for mass spectrometric high throughput biocomputation. The review starts with a brief introduction of proteomics and MS. Computational tools that can be employed at various stages of analysis are presented, including that for data processing, identification, quantification, and the understanding of the biological functions of individual proteins and their dynamic interactions. The challenges of computation software development and its future trends in MS‐based proteomics have also been speculated. Copyright © 2014 John Wiley & Sons, Ltd.     

Polymer lateral diffusion at the solid-liquid interface

Measurements are presented of how polymer surface diffusion at the solid-liquid interface is controlled by surface coverage. The method of measurement was fluorescence correlation spectroscopy (FCS), and the system was poly(ethylene oxide) (PEG) adsorbed onto methyl-terminated self-assembled monolayers in buffered aqueous solution. The translational diffusion coefficient at first increased with increasing surface concentration, presumably because the number of adsorption sites per molecule decreased. Ultimately it slowed by 1 order of magnitude, presumably reflecting jamming by neighboring chains.     

Economy of proficiency testing: reference versus consensus values

Many proficiency tests are operated with a consensus value derived from the participants’ results. Apart from technical issues, one of the reasons often mentioned is that proficiency tests operated with consensus values would be cheaper than those using reference values obtained from a priori characterisation measurements. The economy of a proficiency test must of course be balanced by the need of the participants, and the quality of the comparison in general. The proficiency tests selected in this study had both a reference value and a consensus value, one of which was used for assessing the performance of the participating laboratories. In this work, both a technical and an economical assessment of how the comparisons were operated is made. From the evaluation, it follows that usually the use of consensus values does not necessarily reduce the costs of a proficiency test. However, frequently it may be observed that the quality of the assessment of the laboratories is better with a reference value. Received: 11 October 2000 Accepted: 3 January 2001     

Simplified method for concentration of mitochondrial membrane protein complexes

Extracting and concentrating mitochondrial protein complexes from gel strips after blue native PAGE (BN‐PAGE) can be daunting tasks using the traditional methods, such as electroelution, passive diffusion and centrifugal concentration. We present a simplified gel electrophoresis method to concentrate mitochondrial protein complexes with excellent recovery rate. Mitochondrial complex I present in a long gel strip from BN‐PAGE can be easily concentrated into a 0.8 cm gel strip when a second BN‐PAGE is performed with a Y‐shaped gel and the addition of 0.01% n‐dodecyl β‐D ‐maltoside and 0.001% SDS in the cathode buffer. Once completed, the concentrated protein complex in the gel strip is ready for SDS‐PAGE or proteomic studies.